The Littlest Timelord: Deleted Scenes
by Madison Barton-Maximoff
Summary: Scenes and such that won't make it into my "The Littlest Timelord" series.
1. Bath Time

Bath Time

**A/N - Requested over on my Tumblr: thelittlesttimelord or Elise Smith.**

**Characters: Ten, Elise**

**Summary: The Doctor (Ten) is giving Elise a bath and it doesn't exactly go as planned. **

* * *

"Elise! Come inside!" the Doctor yelled.

The small brunette came running into the TARDIS covered in mud.

They had stopped at a park, but it had been raining.

Elise had run out and started playing, getting mud all over her pants and shoes. The Doctor didn't join her, but he kept an eye on the monitor as she played right outside the doors. Elise found everything interesting, especially when they were on earth. She was a curious child by nature.

In the past few months since the Doctor had found Elise, she had given him multiple heart attacks. It didn't help that this incarnation was filled with anxious energy. Adding a child to the list of things he had to worry about was going to cause him to regenerate. He'd already run off without her multiple times and sometimes he even lost her in the TARDIS, although he suspected the blue box was on Elise's side a lot of the time and kept changing the doors on him to keep her hidden.

The Doctor took one look at her and said, "You need a bath, little one". He picked her up and carried her to the bathroom.

The TARDIS had gone for a bathroom suited to a child. The bathtub had a shower curtain with fish on it, a sink low enough that she could reach it, and a varied selection of bubble baths. The TARDIS had already filled the bathtub and set out some shampoo and conditioner.

The Doctor liked that his blue box had already accepted Elise as her own. "Okay, time to get you out of these wet clothes". He knelt down in front of her and started to remove her shoes, but she stepped out of his reach. "Elise…" he said, about to start scolding her.

She sat down and took off her shoes and wet socks, followed by her pants and the rest of her clothes. When she was done, the Doctor picked her up and put her in the bathtub and wetted down her hair. Elise played with the toys the TARDIS had provided as the Doctor lathered the shampoo into her brown curls.

He rinsed her hair with a cup and did the same with the conditioner, all the while Elise sat there and played quietly.

Elise was a quiet child and the Doctor wasn't sure if she didn't have the ability to speak or if she actively chose not to. But it didn't matter to him. Elise was a Timelord, which meant she was better off with him than someone else.

"There. All done", he said and kissed her head, "Now, I'll be in the control room". The Doctor stood up and dried his hands off on a towel. He needed to work on the console and the TARDIS would alert him if something was wrong with her.

At least the TARDIS had provided a bathroom as close to the control room as possible.

As he turned his back, he felt water hit the back of his head. He turned back around and saw Elise sitting in the bathtub with an innocent look on her face. "You little Dalek", he muttered under his breath as he turned to leave again. He was hit again, but this time he didn't turn around. He knew she wanted him to.

She was doing this to get attention.

He spun around, surprising her and found her filling her mouth with water. "Elise Smith!"

The Doctor took one step towards the bathtub and slipped on the water covering the floor. He went sliding forward and landed in the water right in front of Elise with his legs hanging over the side of the tub.

She laughed as he smoothed his wet hair away from his eyes.

He groaned and rubbed his head.

Elise's eyes went wide in fear and she immediately started crying. She hadn't meant to hurt him! She was only playing!

"Hey, it's okay. I'm alright", the Doctor cooed, "Just a little bump on the head".

She shook her head and he wrapped his arms around her.

"Don't worry about me. I'm just a clumsy old Doctor. We should get you dried off and into bed". The Doctor set her down and climbed out of the tub, before helping her out and wrapping her up in a warm towel courtesy of the TARDIS. He dried off his own hair and said, "See? Totally fine".

Elise gave him a small smile and he led her out of the bathroom.


	2. New Favorite Food

New Favorite Food

**Characters: The Doctor, Elise, Amy Pond, Clara Oswald**

**Summary: Macaroni and cheese would always hold bittersweet memories for Elise.**

* * *

As a Timelord, the Doctor often forgot that humans needed things like food and sleep. And Elise, because she was so young, needed food and sleep about as often as humans.

Today was a lazy day in the TARDIS. They all needed a break from running and nearly dying on every adventure.

It was nearing dinner time and Amy was hungry. She'd only eaten breakfast because she woke up so late. On her way to the kitchen, she stopped off at Elise's room.

The little Timelord was laying in her bed coloring.

Amy wasn't sure where the coloring books and crayons had come from, but she could guess that the little blue box had produced them for her. "Hey you".

Elise looked up from her drawing and smiled.

"Are you hungry?" Amy asked her.

Elise nodded and put down her crayon. She hopped off the bed and followed Amy into the kitchen.

"Okay, what are you feeling like today?" Amy asked, "Fruit? Breakfast?"

Elise just shrugged.

"Ah, I know something you might like". She opened a cabinet and found what she was looking for. Amy shook the box and then showed Elise. "Macaroni and cheese. My mum used to make this for me all the time when I was a child. You'll love it". Amy searched a cabinet for a pot to make it in and filled it with water.

"There you two are", the Doctor said entering the kitchen, "What are we making?"

"Macaroni and cheese", Amy told him, putting salt in the water and setting it aside to boil.

"Good choice". He walked over to the fridge and set to work making fish fingers and custard as Amy worked on making the macaroni and cheese.

Elise smiled seeing the two of them. Without Rory, as much as Elise missed him, it was almost like they were one little happy family. Sometimes she dreamt Amy was her mother, as foolish as it was.

When the noodles were done, Amy poured in some milk, butter, and then cheese powder.

Elise thought the cheese powder was weird, but the macaroni and cheese looked good.

Amy made two bowls and set one in front of Elise.

Her father sat down at the table with his fish fingers and custard.

The two adults watched with bated breath as the little Timelord took a bite of the macaroni and cheese.

Elise swallowed the mouthful and continued to eat it.

"It's good, isn't it?" Amy asked her.

Elise nodded, her cheeks full.

* * *

Years later, Clara entered the kitchen and found Elise. "What are you making?"

"Macaroni and cheese", Elise told her, "It's my favorite food and I was feeling kinda sad today".

"Oh? What about?"

"An old friend of my father's". Elise missed Amy more than she cared to admit.

Clara wondered which one. The Doctor and Elise didn't talk about their past companions very often.

"When I was little, she made it for me whenever we had a lazy day on the TARDIS. Kinda like today", Elise said.

"How old were you?" Clara asked.

"5 or 6 I think. I forget. I'm well over 300 now. I used to imagine we were a family".

"What happened to her?"

"She left. She left, got married, and grew old with her husband". That was how Elise chose to remember Amy. She didn't want to remember the ordeal that had forever tainted Manhattan for her.

"There you two are", the Doctor said entering the kitchen like he had all those years ago. He saw the pot and the box on the counter and froze.

Elise could see the memory cross his mind for a moment before he sat down at the kitchen table. "Want me to make you some fish fingers and custard?" Elise asked her father.

He shook his head.

"Doctor, what's wrong?" Clara asked.

"Nothing", he said smiling, "I just had the greatest idea for an adventure!"

Clara smiled and sat down next to him.

Elise tuned them out as she focused on making her food. Amy had lived a full life with Rory, but she would give anything to see her again. But Amy lived on in her dreams and her memories of the many nights spent making macaroni and cheese.


	3. Family Outing

Family Outing

**A/N - This is more of a "What if...?" than a deleted scene. It was requested over on my tumblr thelittlesttimelord or Elise Smith. Elise is about 9/10 in this, so older than where she currently is in the series. **

* * *

The TARDIS landed and the Doctor opened the doors.

They were in a forest.

"Okay, so not exactly the beach".

Valerie looked over his shoulder. "We can't be far from it".

The Doctor looked down at Elise. "What do you think, Elise? Fancy a walk through the forest?" he asked her.

Elise nodded. "Great!"

The Doctor grabbed the picnic basket and took Elise's hand as they started down the path.

Valerie followed behind them.

The flowers along the path were gorgeous and smelled like something she couldn't quite place.

"Val!" Elise called.

"Coming, love!" Valerie called back. She would pick some of the flowers on the way back and put them in her room.

They finally came to a break in the trees and soil gave way to sand. The beach was completely empty.

"Doctor, are we the only people on this planet?" Valerie asked.

"It was abandoned a millennia ago".

"Can I ask why?"

"I don't quite remember why, but we're safe. I promise".

Usually his promises wouldn't placate her, but she knew he'd never knowingly put Elise in danger. The Doctor chose a spot on the beach and spread out the blanket he'd packed. They sat down and he opened the basket.

The TARDIS had kindly packed all their favorite foods for this picnic. Macaroni and cheese for Elise, fish fingers and custard for the Doctor, and a fruit salad for Valerie.

"Are…are those _pears_ in your salad?" the Doctor asked Valerie.

"Yes. What's wrong with pears?"

Elise stuck out her tongue. "Pears are gross".

Valerie took a bite of her food and found it was still cold. "It's cold!" she said shocked. The walk to the beach hadn't been that short. Her food should have been somewhat warm.

"Of course it is!" the Doctor told her, "This basket is designed to keep hot foods hot and cold foods cold".

The three of them ate their lunch quietly. When they were done, the Doctor put all the containers back in the basket while Valerie wiped Elise's face and fingers. After finishing her macaroni and cheese, she'd decided she wanted some of her father's food and gotten custard all over her.

The Doctor watched as his companion interacted with his daughter. Elise had taken to Valerie straight away, unlike with Amy. Valerie often tucked Elise into bed and read her bedtime stories. She got up when Elise had a nightmare or needed something.

"Daddy? Can I go swim now?" Elise asked, snapping the Doctor out of his thoughts.

"Stay where we can see you. I'll have no regenerations today, you hear me?"

Elise nodded and slipped off her dress, revealing the red and white polka dotted swimsuit Valerie had chosen for her. She ran down to the water and started playing.

The Doctor laid down on the blanket and closed his eyes, trusting Valerie to watch Elise for a while.

"Doctor?" Valerie asked.

"Yes?"

"Does…does Elise have a mum?"

The Doctor opened his eyes and looked at her.

She was glowing in the sunlight. Her blonde hair looked almost white.

"It's a long story", he told her. He explained how he came to care for Elise.

"Wow. Such a strong little girl to escape something like that".

"So Elise doesn't really have a mum. She barely sees River and with River jumping in and out of our lives…"

"That's so sad. Every little girl should have a mother".

* * *

Elise came over to them and collapsed onto her father's lap.

"Are you tired, little one?" he asked her.

Elise nodded and yawned.

"I guess we should get you back then". He picked her up and Valerie grabbed the basket and blanket. As the Doctor carried Elise back to the TARDIS, Valerie picked some flowers along the way.

They were so odd looking, but so very beautiful.

When she got back to the TARDIS, the Doctor was already disappearing down a corridor to put Elise in her bed. Valerie set the basket on the jump seat and smelled the flowers in her hands.

They smelled like…like custard. Fish fingers and custard to be exact.

Earlier she hadn't been able to pinpoint the smell, but she could now.

"Um, Val? Where did you get those flowers?" the Doctor asked her, entering the control room.

"I picked them. They were just so beautiful!"

"And how do you feel?"

Valerie looked at the Doctor.

The sun had tinted his face pink, including his lips.

"I want to kiss you so badly right now". Valerie's eyes went wide and she covered her mouth with her hand.

"Kiss me? Why would you want to kiss me?" he asked, smirking.

"Because I'm in love with you. Doctor, what's going on?"

He laughed. "The flowers secrete truth serum through the leaves and stems. One touch and you can only tell the truth for a few hours".

Valerie dropped the flowers and tried wiping her hands on her jeans.

The Doctor walked over to her and picked up one the flowers.

A pretty blue one and brought it up to his nose. It smelled like pears.

"There's a legend that says the flower's scent changes based on who the person is in love with".

"Fish fingers and custard".

The Doctor smiled. "Pears".

"What?"

The Doctor stuck the flower in her hair and stroked her cheek with his thumb. "I love you too".

Valerie threw her arms around his neck and kissed him.

"Stay with me. Me and Elise", the Doctor told her, "You said it yourself that all little girls need a mother".

Valerie smiled. She couldn't imagine anything better.


	4. First Birthday

First Birthday

**A/N - I imagine this taking place after series 5, but before "A Christmas Carol".**

* * *

"Ellie! Ellie, wake up my little star."

Elise opened her eyes and saw River leaning over her bed. Elise smiled and sat up, throwing her arms around her neck.

River picked her up and carried her into the kitchen, where Amy, Rory, and her father sat at the table.

"Happy birthday!" Amy said, bouncing over to her. Amy placed a tiara on her head and kissed her cheek.

Elise immediately pulled the tiara off her head and tossed it aside.

"Okay then," Amy said, "No tiara."

Her father took her from river and sat her down in her chair.

Rory placed a plate of waffles with a candle in front of them and Amy lit it with a match.

"What you do is make a wish and then blow it out," her father told her, "It's an earth tradition."

Elise may have been a Timelord, but the Doctor and River, along with Amy and Rory, raised her as they would a human child. So in reality, she was equally human and Timelord. She closed her eyes and made her wish.

"Now you can't tell anyone or it won't come true," Amy told her.

Elise knew her wish couldn't come true anyway. It was an impossible wish.

"Now eat up!" her father told her, "Lots of fun activities planned for today!"

* * *

The Doctor opened the doors to a vast playground filled with kids.

Elise stepped out of the TARDIS, her hand in River's.

"Go on," her father told her.

But Elise's eyes were drawn to an odd shaped building across the street from them. Elise pointed at it.

"Seriously?" the Doctor asked.

"What? What is it?" Amy asked.

The Doctor groaned. "A planetarium."

"If Elise wants to go to the planetarium, then that's where we're going," River said.

"But I can show her the real stars!"

Elise looked at him with her big blue eyes and the Doctor sighed.

"Okay."

Elise smiled and took her father's hand as they walked over to the building.

They went inside and Amy and Rory paid for the tickets, including one to a show about constellations.

There was a long corridor reminding Elise of the TARDIS.

The walls were painted with pictures of the planets of the solar system with facts about them that Elise ignored. It led to an indoor playground with models of spaceships.

"Do you want to go play?" River asked her.

Elise shook her head.

The children were pretending to kill aliens like in the movies.

She and the Doctor were aliens.

Humans didn't understand that most aliens were just like them, with a few exceptions. They just wanted to live their lives and raise families.

It was times like this that Elise was acutely aware that she'd never fit in with humans. She saw the world differently and that made it hard to have friends who didn't understand.

* * *

The next section of the planetarium was all about the moon landing and the Mars Rover. There was also a screen that let you look at the surface of Mars.

The Doctor walked over to one of the screens and discreetly pulled out his sonic screwdriver. He picked Elise up and set her on his hip as they watched the screen.

Elise's eyes went wide as she watched Gallifrey appear.

"Not the same, I know. I wish I could make your birthday wish come true," he told her. The Doctor had guessed her wish, because it was something he wished every day. That he could go back. Especially now he had Elise. He'd give anything to go back to Gallifrey and raise her there. Have her go to the Academy and learn about the laws of time and the universe. He was startled out of his thoughts by a hand on his shoulder.

"The show starts in 15 minutes," River told him.

They entered the large auditorium and Elise laid down on the floor, staring at the domed ceiling.

River and the Doctor laid down on either side of her.

Rory and Amy sat over in the chairs, giving the small family some space.

Before they entered, River had pulled the Doctor aside and made him promise to keep his mouth shut. This was Elise's present. If she wanted to know more, he could teach her later.

But instead of paying attention to the presentation, the Doctor watched Elise the whole time. He loved how her eyes lit up as the stars created pictures and the smile on her face as the presenter told them facts about the constellations. The love of space flowed through her veins and even though much of information was wrong, it still made the Doctor happy to see Elise enjoying herself.

* * *

**Feel free to request anything you'd like to see. You can request here or leave it in a review on the main story.**


	5. Orion

Orion

**A/N - Request by anon on the last chapter.**

* * *

It was a quiet day in the TARDIS.

Amy and Rory were at home enjoying wedded bliss, so it was just Elise and the Doctor traveling alone.

The Doctor was down below the console while Elise sat on the stairs near him, sketching River.

There hadn't been a lot of adventures lately so there was nothing to put in her diary.

"Dad?" Elise asked.

"Yes?"

"Could we get a pet for the TARDIS?" She'd been wanting a pet ever since staying at Craig's.

The Doctor smiled and jumped out of his swing. "What are you thinking?" he asked her as he ran to the console.

"Something unique," she told him.

He threw a lever and the TARDIS took off. When they landed, he grabbed Elise's hand. "Close your eyes," he told her.

Elise closed her eyes and he opened the doors.

"Open them."

Elise opened her them and saw they were right in front of a pet shop. Elise smiled and they went inside.

"Pick out anything you want," he told her. Instead of bringing her to a normal pet shop filled with animals like puppies, kittens, and bunnies, he had brought her to a more exotic pet shop.

It had lizards, snakes, turtles, and other more unique pets.

He watched as she looked at the turtles until she heard something rattling around in a cage.

In the back was a black owl with large orange eyes. It had white specks on its feathers, almost like a reverse Hedwig.

"Hello," Elise said.

The owl hooted at her.

"Careful, he bites," the owner said, "Hates everyone."

Elise stuck her fingers into the cage and the owl gently nipped at them. Elise laughed.

The bird wasn't mean. He was probably just misunderstood and needed some love and patience.

"You want him?" the Doctor asked her.

Elise nodded enthusiastically.

The Doctor turned to the owner. "How much?" he asked.

"For you? He's free."

"Really?" Elise asked.

"I've had that bird for almost three years and in all that time, he's never taken to anyone like you. You'd be doing me a favor." The owner took the owl from the cage and placed him into a carrier.

The Doctor picked up the carrier and they went back to the TARDIS.

"Don't we need food?" Elise asked her father as he opened a door.

It was a forest.

"I'm sure he can find some mice in here," the Doctor said. He walked over to a shed and pulled out some leather gloves. He knelt down and slipped them onto Elise's hands. "You'll need to wear these whenever you handle him so his talons don't cut up your hands and arms," he told her.

He opened the carrier and the owl flew to Elise and perched on her hand. She stroked his chest with her other hand.

"What are you going to call him?" the Doctor asked.

Elise thought for a moment before she said, "Orion."

"After the constellation?" Elise nodded.

His name would be a reminder of her birthday trip to the planetarium. Orion nipped at her hair before he flew off.

Elise turned to her father and threw her arms around his waist. "Thank you."

"You're welcome, Ellie."

"I can't wait to tell River!"

"Hey, take your gloves off first."

Elise slipped them off and the Doctor took them.

"Well go on," he told her.

Elise ran out of the room heading back to the console room to call River.

The Doctor put the gloves away in the shed. When he came back into the console room, Elise was sitting on the jump seat. "Elise, what's wrong?"

"They wouldn't let me talk to her."

The Doctor hugged her and said, "Maybe we can try again later. Why don't we jump ahead and go get the Ponds?" He stood up and went to the controls, thankful his back was to her. He knew their lifestyle wasn't always ideal, but it still broke his hearts when she was sad and he couldn't do anything about it. But then an idea hit him. He flipped a lever and said, "Come along, Elise!"

Elise followed him out of the TARDIS. She smiled when she saw River. Elise ran up to the bars and started to tell her all about her new pet.

"Doctor Song isn't allowed visitors right now," a guard said.

"Five minutes. That's all I'm asking for," the Doctor said.

The guard looked at the little girl talking to River. "Fine. Five minutes."

The Doctor approached them.

"What did you name him?" River asked Elise.

"Orion. Like the constellation."

"Just couldn't say no to her could you?"

"Almost every child has a pet while growing up," the Doctor told her.

"I'm just surprised it's not from some other planet."

"I can be responsible when I want to."

"Of course you can, sweetie."

"Elise, I need to talk to River alone. Why don't you go clean up your room?"

Elise looked at River.

"Mind your father. I'll see you soon, okay?" River said.

Elise tapped River's forehead with her own. It was something Elise had started doing since the Byzantium. Every time she saw River, she would share memories from various adventures.

River kissed her cheeks and said, "Run along."

Elise went back to the TARDIS and River stood up.

"What's wrong?" River asked him.

The Doctor sighed. "I wish you could travel with us full time. Elise needs her mother."

"Mother?"

"Don't play coy River. You know Elise looks at you as a mother figure. More so than Amy."

"What's brought this on?"

"After she got Orion, the first thing she wanted to do was tell you but they wouldn't let you talk to her. You should've seen her face, River. She was heartbroken."

"Times up!" the guard yelled.

"I'm sorry, sweetie," River told him.

The Doctor smiled sadly. "I know you are." He leaned forward and kissed her forehead. "Till next time, Doctor Song."

"Till next time, Doctor."

The Doctor entered the TARDIS and found Elise waiting for him. "We have some Ponds to pick up, don't we?"

Elise gave him a small smile and nodded.

The Doctor threw the lever and they took off.

* * *

**Thank you so much for this request! I really loved writing this. Please feel free to leave other requests.**


	6. Angel

Angel

**A/N - This was requested over on my Tumblr thelittlesttimelord or Elise Smith. This is a one-off and does not affect the canon of the story.**

* * *

Elise and the Doctor left the TARDIS.

They had landed in some type of forest.

"Um, are we supposed to be here?" Elise asked.

"Well the TARDIS said we landed in the correct place. There should be a temple around here somewhere."

"Are you sure we're in the right time?"

"Where's the fun in that?"

Elise rolled her eyes. It was honestly a miracle he'd made it this far and was still alive.

They started walking and eventually came to a clearing with a like.

Someone was swimming in the lake.

"Excuse me?" the Doctor asked.

The person swam closer to them and they realized it was a woman.

She had blonde hair, nearly platinum, and her eyes were a bright blue. It almost looked like they were glowing. "Hello!" she said. Her voice was high pitched and airy.

"Hello, we were wondering if this was Anheliv?" the Doctor asked.

The woman climbed out of the water, revealing the long white gown she was wearing that was now clinging to her bod. She also had feathery white wings on her back.

"So where exactly are we?" Elise asked, "You didn't really explain."

"We're on Anheliv, which roughly translate to Planet of the Angels."

"So she's an angel?" Elise asked.

"Not exactly. Everything in human history or culture came from somewhere. What's more likely is that some of them found their way to earth and they became what humans now think of as angels."

"What are you?" the woman asked.

"We're Timelords," the Doctor said.

"Timelords? I thought they were a myth."

The Doctor's mouth dropped open in surprise. "A myth?"

"What's your name?" Elsie asked the woman.

"Inger."

"Is there a temple around here somewhere, Inger?" the Doctor asked.

Inger nodded and motioned for them to follow her.

"Do you have any shoes you can put on?" the Doctor asked Inger, worried about her feet getting cut up.

Inger shrugged. "I prefer to feel the ground beneath my feet."

As they walked, Elise reached out and stroked one of Inger's wings.

Inger lifted her wing and tickled Elise's nose with the tip. Elise laughed.

When they came upon the temple, the Doctor noticed it was covered in vines and shrubbery. "What happened?" he asked.

"The temple has been abandoned for hundreds of years," Inger said.

They entered the temple and Inger walked up to the altar. She snapped and a small flame appeared on the tip of her finger. She lit a candle and whispered a quick prayer. "Our people stopped worshiping the gods three hundred years ago, but I come here sometimes on my own. Sometimes I pray, other time I just sit here in silence. But mostly I just tell them about my day." Inger looked over at Elise and the Doctor. "You think I'm crazy."

"What? No, we don't," Elise told her.

"It's okay. Most people think I am. I don't mind it."

Elise sat down on the bench next to her. "We all need something to believe in sometimes. Otherwise, what's the point in living?"

"What do you believe in?"

Elise looked over at the Doctor. She'd never believed in anything. Not even when she lived with her real mother and father on Gallifrey. But if there was one thing she believed in, it was the Doctor.

* * *

After visiting the temple and learning more about Inger and her people (and sketching the temple along with several of its sculptures), Elise and the Doctor started to walk back to the TARDIS.

"Would you like to travel with us?" the Doctor asked Inger.

"Travel with you?"

"You don't fit in here. We know what that's like."

"But…but I can't just leave my family."

The Doctor patted the door of the TARDIS. "See, the great thing about this police box, is that she's a spaceship _and_ a time machine. We can leave now and travel for hundreds of years and drop you off five minutes from now."

"With my help, of course," Elise added. Elise was just learning how to fly the TARDIS and already she'd landed her with the upmost precision.

"But why?" Inger asked.

"I never know why, I only know who," the Doctor said, "Step inside these doors and have your eyes opened to all the wonders around you." The Doctor opened the door to the TARDIS and Inger entered, the Doctor and Elise following.

"This is amazing!" she said spinning around.

"Next stop, the universe!" the Doctor said, throwing a lever, "Geronimo!"

Inger giggled as she was thrown to the floor as the TARDIS took off.

The Doctor smiled seeing her enjoy herself. She would be the perfect companion for himself and Elise. He could tell.


	7. Never Gonna Be Lonely

Never Gonna Be Lonely

**A/N - I wrote this for a writing challenge on Tumblr. I imagine this taking place in book three when Elise and the Doctor travel alone without the Ponds.**

* * *

"I'm headed to bed," Elise told her father.

The Doctor looked up from what he was doing under the console platform. "Huh?"

"I'm going to bed."

"Okay. Sleep well."

As Elise left him, she could tell something was on his mind. Even though they'd spent well over three hundred years together, there were still times where he'd space out and she could tell his mind was elsewhere. But he never let on as to what was going on.

The Doctor soniced another cable and it sparked. He threw his screwdriver at the wall in frustration and got out of his swing. He didn't even really know what he was doing in the first place. It was just something to keep him occupied during the quiet moments. When it was quiet, his mind had the tendency to stray into dark places.

He shrugged off his jacket and threw it in the jump seat before walking over to the doors of the TARDIS. He opened them and sat down, staring out into space. As calming as it was, it also produced feelings of loneliness. As one of the last living Timelords, the Doctor often felt lonely. Even with his adoptive daughter Elise.

The Doctor hated to be alone, because it meant he thought about his family. The one he had condemned to death on Gallifrey. But every time he looked at Elise, he was reminded that he had also condemned her and her family to the same fate. She'd still be in the Timelock if it wasn't for Rassilon and the other Timelords. He thought about his companions. The ones that had died and the ones who left of their own free will. He didn't know how long he had been sitting there until he heard footsteps.

"Okay, what's wrong?" Elise asked, entering the console room.

The Doctor patted the space next to him and she sat down.

"You've been spacey all day. You gonna tell me what's on your mind?"

"Just thinking," he told her.

"About?"

"My family."

Elise was shocked. Usually he'd make up a lie, but for once he was being honest. "Do you remember what they looked like?" Elise asked.

"Of course." He remembered his children. His grandchildren.

"I don't."

The Doctor looked at her. He expected to see tears in her blue eyes, but there were none.

"I don't remember what my father and mother looked like. I don't remember the sound of my mother's voice. There's just nothing," Elise told him.

She spoke of them in a cold detached manner. Almost as if it had happened to someone else. But he wasn't really surprised. She was four when he met her. Even human children had trouble remembering that far back.

"Do you want to?"

Elise looked at him. "Honestly? No. Not really. It's been, what? Almost 250 years? What would be the point? You and River are my parents now."

"It's always good to remember where you came from."

"As far as I'm concerned, my life started the moment I met you."

The Doctor smiled and kissed her forehead. His life had certainly been improved by her presence. It had been so long since he had been a father, but he loved teaching Elise all that he knew. He was contented with the fact that the Timelords would continue on in some capacity thanks to her, should she ever have children.

"Do you ever wonder what life would have been like? If the Time War had never happened?" Elise asked, "If our families hadn't died?"

"I probably still would have run away. I was too different."

"Maybe we would've met."

"But maybe we wouldn't have."

"That night Amy ran away with you…us. You told her it was because you were lonely."

"I was."

"I can promise you one thing as long as I'm alive, **_you're never gonna be lonely_** again."

The Doctor wrapped an arm around her shoulder and kissed her head. He would never be lonely again, but she would soon. Because he was on his last regeneration and she had no idea.


	8. Deleted Scene from Day of the Moon

Deleted Scene from "Day of the Moon"

**This takes place before Chapter 7.**

* * *

"Ellie, you're going to go with River," the Doctor said.

Elise turned to her father and shook her head. "What? No. I wanna stay with you."

The Doctor sighed. "You can't." He knelt in front of her. This would hurt him more than it would hurt her. At least she'd be with someone she knew and could keep her safe. But whenever she was away from him, he felt like part of himself was missing. "It'll only be a few months."

This would be the longest time they had ever been apart.

Elise wrapped her arms around his neck and set her temple on his.

The Doctor was hit with a wave of sadness and he had to squeeze his eyes shut to stop the tears. Elise felt everything so strongly.

"Elise…" River said. She put her hand on Elise's shoulder. "Sweetie."

The Doctor pulled away from Elise and wiped her tears with the cuff of his jacket. "Be a good girl for mummy, okay? Do everything you're told."

Elise nodded and sniffled as she wiped her eyes.

"Hey. It'll be over before you know it. After this is all over, we'll go somewhere. Just me and you, okay?" The Doctor kissed her forehead before she stepped out of the TARDIS with River. As he put the TARDIS in flight, he couldn't help but feel like he was leaving one of his hearts with her.


	9. Mother's Day

Mother's Day

* * *

Elise entered the control room, but there were no Ponds. "Dad, where are the Ponds?" she asked. She was pretty sure they were supposed to be picking them up today. She and her father took trips alone every once and a while, but it seemed like they hadn't seen them in a while.

The Doctor looked up from where he was working on the console. He'd been trying to install a new control, but it wouldn't do what he wanted it to. "It's a holiday today. Mother's Day or something. Most people take their mother out to eat and give her presents."

Mother's Day?

"Could…could we celebrate with River?"

The Doctor smiled. "Of course. Just let me call Stormcage." He needed a break anyway.

Elise smiled and ran back to her room. She dug through her drawings and found what she was looking for. She'd finished it weeks ago, but now she had the perfect opportunity to give it her. When she came back in, River was standing in the control room. Elise ran to her and hugged her.

"You seem to grow taller every time I see you."

Elise presented the canvas to her. It was a portrait of River, done in beautiful watercolors. "Happy Mother's Day!"

River smiled and took it from her. "Oh! Thank you, sweetie. I'll put it up in my cell once we get back."

"So, I thought we could go for a picnic," the Doctor said, flipping a lever.

The TARDIS landed roughly and they stepped out. They were in a park and it looked like it was Earth.

The Doctor laid down a blanket and River set down the basket. She pulled out the food, fish fingers and custard for the Doctor or course and macaroni and cheese for Elise, and a bottle of wine for herself.

"Are you not eating?" Elise asked.

"Not hungry right now, sweetie. Now, tell me all about the adventures you've been having."

Elise pulled out her diary and read off some of the adventures they had as they ate. River smiled seeing that her diary looked exactly like hers and the Doctor's.

River may have not been Elise's biological mother, but she was her daughter in every sense of the word.

* * *

Soon, it was time for River to return to Stormcage.

They walked River back to her cell. She hung Elise's picture up next to her bed, so she'd see it every morning when she woke up. "Perfect!"

"I wish we didn't have to leave you here," Elise told her. She was used to leaving River, but it never failed to hurt.

River tucked some of her brown hair behind her ear. "I know, sweetie. But we'll be together again soon. I promise." She hugged Elise and said, "Now, keep your father out of trouble."

"Oi!" the Doctor said.

Elise laughed. River winked at Elise.

"I'll try," Elise told her, "Goodnight, mum."

"Goodnight, Elise."

Elise went back inside the TARDIS.

"You know, the more Elise grows, the more she reminds me of you," the Doctor told River.

"Is that a good thing or a bad thing?"

The Doctor smiled and tucked one of River's curls behind her ear. "She's her mother's daughter."

River grabbed him by his jacket lapels and kissed him. The Doctor returned the kiss and River pulled away. "Goodnight, Doctor."

The Doctor cleared his throat and ran a hand through his hair. He straightened his bowtie and said, "Goodnight, Doctor Song." No matter how many times they did that, she still made him feel all flustered. He stepped back into the TARDIS.

Elise was sitting in the jump seat, sketching in her notebook.

"So, shall we jump ahead and get the Ponds?" he asked.

* * *

River watched the TARDIS disappear and then sat down on her bed. She reach under it and pulled out her diary. She thumbed through it until she found the entry she was looking for.

A letter was tucked in there, along with a picture.

_Dear River,_

_God, you were right! I know you're probably smirking your pretty little ass off. Knock it off. As soon as I saw his eyes and heard him talk, I knew he was the one for me. He's perfect! But you already knew that huh? We'll be sure to drop by and spend Mother's Day with you, okay? He and dad don't really get along, but what's new? I don't have much time to talk right now, but know that I think about you often. I think you'd really like him. Dad's calling for me, so I've got to go now. _

_Love, _

_Elise_


	10. Letting Go

Letting Go

* * *

Elise awoke to yelling. It was something she was very familiar with. She got out of bed and made her way to the control room.

It was River and her father.

"If you had just listened to me…!" River yelled.

Elise sat down at the top of the stairs watching River and her father go at it. She loved seeing them bicker, but this was just fighting. She knew the Doctor would never lay his hands on River, but she still hated to see people fighting.

"You know what? I'm not going fight with you anymore," River said.

The Doctor laughed bitterly. "Oh? And why's that? I thought you just loved to."

River looked at him and then her eyes met Elise's.

The Doctor spun around and saw her sitting there. "Elise…" he breathed with wide eyes. He knew how fighting affected her. "I…We…"

"I woke up and heard you two fighting…" She stared down at her hands. She didn't cry or say anything else, but the Doctor could see that she was upset.

River walked up the steps and sat next to Elise. "Ellie." River played with the ends of Elise's hair. "My little Ellie."

"It's fine," Elise said.

The Doctor sighed. "No, it's not." He sat down on the other side of her. "River and I didn't mean to wake you. We shouldn't have been fighting in the first place."

"But you know how your father is."

"Oi!"

Elise laughed and smiled.

"Come on. Let's get you back to bed," River said. She helped Elise up and they walked down the corridor to Elise's bedroom.

It had changed once again. Gone was the play area and in its place was an expansive collection of art supplies. A large canvas sat against the wall. It was of a nebula. The same one floating outside her window.

River knew they were parked somewhere and not drifting through the vortex.

"It's a fake window. The TARDIS shows me what I want so I can paint it," Elise explained.

"It's really good."

"Thanks, mum."

Elise climbed back in bed and River sat next to her. Elise rolled over and put her head in River's lap.

River stroked her daughter's hair. "You shouldn't have to listen to us fight."

"Mum, stop apologizing."

"Sorry, sweetie."

"Will you sing something to me?"

"Do you want your usual?"

Elise closed her eyes. "Sing me something new."

River settled on an ancient lullaby she'd come across in her work. Apparently it was extremely old, because the TARDIS wasn't translating it.

But the melody was pretty and Elise was asleep in no time.

* * *

When Elise was asleep, River got up and went back into the control room. "Well she's asleep," River told the Doctor.

The Doctor was quiet.

"Doctor?" River approached him and put a hand on his arm. "It's okay."

"No. It's not. Fighting bothers her. God, when she was a child she used to cry when I even raised my voice."

"She seemed fine when she fell asleep."

"You don't understand, River! You're not with her every minute of every day!"

"Will you lower your voice?"

The Doctor sighed and ran a hand through his hair. As much as he loved River, she still seemed to get under his skin.

"Now what is this really about?" River asked.

"Elise is growing every day. Soon, she won't need me anymore and she'll leave. They always leave."

"Sweetie…" River wrapped her arms around him.

They both knew a little bit about where Elise's timeline was heading. It was just a question of "when".

"Elise loves you, you know that. But she's a young woman now."

Elise had just turned 400, putting her in her late teens in human years.

"Even if she leaves, you know it won't be for long."

The Doctor pulled away, but there were tears in his green eyes. "But she'll get married and probably have children. Then she won't need me anymore."

"She'll always need you. She needs you more than anyone in the universe. You're the most important thing to her. Just try and enjoy the time you have with her and not worry about the future."


	11. Fear is a Superpower

Fear is a Superpower

**A/N - Requested on my Tumblr. This is obviously young Elise. Since she talks in this piece, it takes place during series 6, but before "The Doctor's Wife" since she has no idea what happened to the Timelords yet.**

* * *

_Elise ran through the streets. Buildings burned and crumbled around her.  
_

_She had no idea where she was. Where were her parents?  
_

_Children around her screamed for their mothers and fathers, so where were hers?  
_

_Elise ran down a dark alley to escape the chaos.  
_

_Something was already there.  
_

_"H…Hello?" she called. Elise watched in horror as a Dalek rolled towards her.  
_

_"EXTERMINATE!"_

* * *

Elise sat up in bed, tears streaming down her face. She looked around her and found that she was safe. She was in the TARDIS and not on Gallifrey.

Elise got out of bed and walked down the silent corridor towards the control room.

The Doctor sat on the jump seat, reading a book. He heard Elise sniffle and looked up. He quickly put his book down and rushed over to her. "Elise? What's wrong?" he asked.

The question made her start crying again.

He picked her up and held her close to his chest. He walked over to the console and pressed a button.

Soft music filled the control room.

"There, there, my little Ellie." The Doctor gently swayed back and forth and rubbed her back to try and calm her. "It's okay." He pressed his temple against hers and saw the nightmare. "You know I'd never let anything like that happen to you."

After a while, Elise calmed down and the Doctor carried her back to her bedroom. He laid her down in her bed and kissed her head. As he turned to leave, he heard, "Daddy?"

"Yes, Elise?"

"Have you ever been scared?"

A feeling of dread filled the Doctor. He walked back over to her bed and sat down.

Elise curled up in his lap.

"Yes."

"Really? I thought you weren't scared of anything."

"Once, when I was little, I escaped to a little barn outside near where I lived."

"Why?"

"I was almost at the age where I would enter the Academy. Most Timelords go to the Academy or join the Army. This was before the Time War. But most joined the Army after leaving the Academy. Of course, I didn't want to go into the Army. I wanted to help people."

"That's why you call yourself the Doctor!"

The Doctor smiled. "Yes. Anyway, I went out there to cry so no one would hear me. I heard a man's voice calling out for someone. So of course I sat up in bed and asked who was there. I started to get out of bed and when I did, a hand grabbed my ankle."

Elise gasped at this.

"I was terrified. But then a voice told me it was just a dream. It told me to lay back down and go to sleep. But before I fell back asleep, the voice told me to listen. It said, _I know you're afraid, but being afraid is alright. Because didn't anyone ever tell you, fear is a superpower. Fear can make you faster and cleverer and stronger and one day, you're gonna come back to this barn and on that day, you're going to be afraid indeed. But that's okay, because if you're very wise and very strong, fear doesn't have to make you cruel or cowardly. Fear can make you kind."  
_

Elise was quiet as the Doctor stroked her hair. "Did you go back to that barn?"

"Yes. I did."

"And what happened?"

The Doctor kissed her head. "I made the hardest decision I ever had to make." He didn't explain any further. He didn't know when he'd tell her, but now was not the time.

The Doctor laid her back down in her bed and covered her up, before sonicing her ceiling to look like the night sky. "Time to go to sleep, little one. And remember, it's okay to be scared." He kissed her forehead, thanking whatever gods existed that Elise had fallen into his life. That he wasn't alone anymore. Something good had come out of the Time War.

But voice had been right about one thing.

In his old age, fear made him kind.


	12. Don't Wander Off

Don't Wander Off

**A/N - Inspired by a picture sent to me by my friend on Tumblr and the subsequent conversation we had.**

* * *

Amy, Elise, and the Doctor stepped off the TARDIS.

"A market. You've brought us to a market?" Amy asked.

"Not just a market. My favorite market. I came here with my granddaughter once," the Doctor said. He started to walk off.

"Wait. Granddaughter?" Amy called, running after him.

Both of them forgot little Elise by the TARDIS.

Elise didn't know what to do. Should she wait for the Doctor and Amy to realize she was gone? Or try looking for them?

Elise stood there for a moment before she decided. She would try to find them herself. She stepped into the crowded alleyway, her eyes peeled for a redhead or red bowtie.

As she walked around the market, her eyes landed on a TARDIS. She knew it wasn't the one she arrived in, so what was another one doing here?

The Doctor had mentioned he'd been here once before, so maybe it was another version of him.

Elise knocked on the door.

The door swung open.

"What?" the tall, gray haired man snapped. He looked down at her and sighed angrily. He quickly closed the door. "It figures that floppy hair would lose you."

Elise looked up at him.

He had large eyebrows and was much older than her father. He also sounded like Amy. Scottish. "I suppose we should try to find your family. Come along, little one."

Elise smiled. Her father called her the same thing.

The man started walking towards the market and Elise caught up with him. She wrapped her small hand around his.

"No. No hand holding. I'm against hand holding," he said, but didn't pull his hand away.

They walked through the market. They passed many food stalls and Elise could feel herself getting hungry. She tugged on the man's hand.

"What is it now?" he asked her.

Elise pointed to her tummy.

He rolled his eyes. "Right, this is when you didn't speak," he muttered.

Elise furrowed her eyebrows. They hadn't met before. She knew this man must have been another Doctor, but she didn't recognize him.

The man steered them over to a food stall, where he bought her a strange fruit. "You'd better eat that, because I'm not buying you anything else."

Elise glared at him for being so rude, but ate the fruit anyway.

* * *

The man and Elise walked for a little longer, before Elise spotted the Doctor and Amy.

"Go on, little one," the man told her.

"Elise!" the Doctor said, rushing forward. He gathered Elise in his arms and picked her up. "I am so sorry."

Elise smiled and placed her hand on his cheek, showing him that she was okay.

"You just had your own little adventure, didn't you little miss?" Amy asked.

Elise nodded and set her head on her father's shoulder as he carried her back to the TARDIS. She saw the older man in the crowd and waved at him.

The man waved back and gave her a small smile. The Twelfth Doctor waited until his former self took off in the TARDIS, before Elise and Bill walked up to him.

They were both eating ice cream.

"Where have you two been?" he asked.

"Exploring like you told us to," Bill told him.

"Did I hear the TARDIS? Did you move her?" Elise asked.

The Doctor debated whether or not he should tell her in encountered a younger version of herself.

He was thankful that his former self had left. He knew he wouldn't have been able to stop Elise if she had seen the man who raised her. She still missed him and the Doctor knew this. He could see it in her bittersweet smile when she brought up Amy and Rory or River.

But if young Elise had met the current Elise, there was no telling what may have happened.

Maybe Elise remembered, but just wasn't saying anything to avoid the awkwardness of having to explain it to Bill.

"Come on you two. We should be getting back before Nardole realizes we're gone."


End file.
